Mercurial > repos > recetox > matchms_metadata_export

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a57d984a9850c1faa44b6948981eb1303881ba9c
author recetox
date Thu, 14 Aug 2025 12:42:38 +0000
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1 <tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="MIT">
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2 <description>extract all metadata from mass spectra file to tabular format</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>help.xml</import>
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6 </macros>
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7 <expand macro="creator"/>
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8 <expand macro="bio.tools"/>
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
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12 </requirements>
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14 <command detect_errors='aggressive'><![CDATA[
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15 python3 '${matchms_python_cli}'
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16 ]]></command>
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18 <configfiles>
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19 <configfile name="matchms_python_cli"><![CDATA[
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20 import matchms
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22 from matchms.importing import load_from_msp, load_from_mgf
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23 from matchms.exporting.metadata_export import export_metadata_as_csv, export_metadata_as_json
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26 if "$harmonize_metadata" == "False":
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27 matchms.Metadata.set_key_replacements({})
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29 spectra_list = list(load_from_${input_file.ext}("${input_file}", $harmonize_metadata))
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30 print(f"Loaded {len(spectra_list)} spectra from ${input_file}.")
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32 #if $out_format == 'tabular':
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33 export_metadata_as_csv(spectra_list, "${output_file}", delimiter="\t")
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34 #else if $out_format == 'csv':
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35 export_metadata_as_csv(spectra_list, "${output_file}", delimiter=",")
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36 #else if $out_format == 'json':
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37 export_metadata_as_json(spectra_list, "${output_file}")
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38 #else
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39 print(f"Unknown output format: $out_format")
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40 #end if
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41 ]]></configfile>
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42 </configfiles>
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44 <inputs>
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45 <param label="Spectra file" name="input_file" type="data" format="msp,mgf" help="Mass spectral library file."/>
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46 <param label="Harmonize metadata" name="harmonize_metadata" type="boolean" truevalue="True" falsevalue="False"
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47 checked="false" help="Apply harmonization process on the metadata keys (e.g. parse numeric values, derive precursor mass)."/>
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48 <param name="out_format" type="select" label="Output format" display="radio" help="Output format for the metadata file">
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49 <option value="json">json</option>
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50 <option value="csv">csv</option>
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51 <option value="tabular" selected="true">tabular/tsv</option>
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52 </param>
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53 </inputs>
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55 <outputs>
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56 <data label="matchms extract metadata on ${on_string}" name="output_file" format="tabular">
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57 <change_format>
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58 <when input="out_format" value="json" format="json" />
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59 <when input="out_format" value="csv" format="csv" />
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60 </change_format>
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61 </data>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="input_file" value="convert/mgf_out.mgf" ftype="mgf"/>
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66 <param name="harmonize_metadata" value="True"/>
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67 <output name="output_file" file="convert/metadata.tsv" ftype="tabular" compare="sim_size" delta="0"/>
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68 </test>
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69
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70 <test>
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71 <param name="input_file" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
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72 <param name="harmonize_metadata" value="True"/>
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73 <param name="out_format" value="csv"/>
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74 <output name="output_file" file="convert/metadata.csv" ftype="csv" compare="sim_size" delta="0"/>
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75 </test>
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76
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77 <test>
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78 <param name="input_file" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
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79 <param name="harmonize_metadata" value="False"/>
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80 <param name="out_format" value="json"/>
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81 <output name="output_file" file="convert/metadata.json" ftype="json" compare="sim_size" delta="0"/>
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82 </test>
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83 </tests>
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84
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85 <help>
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86 Documentation
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87 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
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88 This tool can be used to export the metadata accompanying the actual spectral to a tabular file,
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89 creating a column for each attribute and a row for each spectrum.
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90 All keys which are present in at least one spectrum are contained in the output.
f04610d25411 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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91
f04610d25411 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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92 @HELP_matchms@
f04610d25411 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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93 </help>
0
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94
dfdbccfa8753 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit c10d901c526d0895869d18a1d1bdd1ea58ed7473
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95 <expand macro="citations"/>
dfdbccfa8753 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit c10d901c526d0895869d18a1d1bdd1ea58ed7473
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96 </tool>